def source_create(request, template_name='source/source_form.html'):
if request.method == 'POST':
form = SkipperForm(request.POST)
if form.is_valid():
source = Source()
source.text = form.cleaned_data['text']
source.title = form.cleaned_data['title']
source.owner = request.user.first_name + ' ' + request.user.last_name
source.save()
# Now build it.
build(user=request.user, sourceobj=source)
cache.clear()
return redirect('source_list')
else:
return render(request, template_name, {'form': form})
else:
default = '''
coordinator "Name" "Email" "Url"
contact "Email"
description {
}
'''
form = SkipperForm({'text': default, 'title': 'New Role'})
return render(request, template_name, {'form': form})
def source_create(request, template_name='source/source_form.html'):
if request.method == 'POST' :
form = SkipperForm(request.POST)
if form.is_valid():
source = Source()
source.text = form.cleaned_data['text']
source.title = form.cleaned_data['title']
source.owner = request.user.first_name + ' ' + request.user.last_name
source.save()
# Now build it.
build(user=request.user, sourceobj=source)
cache.clear()
return redirect('source_list')
else:
return render(request, template_name, {'form':form})
else:
default = '''
coordinator "Name" "Email" "Url"
contact "Email"
description {
}
'''
form = SkipperForm( {'text': default, 'title': 'New Role'} )
return render(request, template_name, {'form':form})
def test_form_template(self):
template_params = {
'name' : 'page12.html',
'content' : 'test'
}
template = Template(**template_params)
template.save()
source_params = {
'source' : 'test-source',
'slug' : 'test-source'
}
source = Source(**source_params)
source.save()
form_params = {
'name' : 'test',
'slug' : 'test',
'template' : template,
'form_type' : source,
'height' : '100',
'width' : '200'
}
form = ContactForm(**form_params)
embed_code = """<iframe style="border: none;
overflow: hidden;" src="page12.html" frameborder="0"
scrolling="no" width="200" height="100"></iframe>"""
assert form.embed_code == embed_code, True
def upload_opml_file(request):
if request.method == 'POST':
form = UploadOpmlFileForm(request.POST, request.FILES)
if form.is_valid():
#opml_file = request.FILES['file'].read()
#tree = ET.parse(opml_file)
#root = tree.getroot()
#for outline in root.iter('outline'):
# source = Source(user=request.user, xml_url=outline.get('xmlUrl'))
# source.save()
Source.objects.all().delete()
Group.objects.all().delete()
group = None
for event, elem in ET.iterparse(request.FILES['file']):
#import pdb; pdb.set_trace()
if elem.tag == 'body':
outlines = list(elem)
for outline in outlines:
if 'xmlUrl' not in outline.attrib:
group = Group(user=request.user, name=outline.attrib['title'])
group.save()
children = list(outline)
for child in children:
source = Source()
source.text = child.attrib['text']
source.title = child.attrib['title']
source.feed_type = child.attrib['type']
source.xml_url = child.attrib['xmlUrl']
source.html_url = child.attrib['htmlUrl']
source.save()
user_source = UserSource(user=request.user, source=source, group=group)
user_source.save()
elif 'xmlUrl' in outline.attrib:
print outline.attrib
source = Source()
source.text = outline.attrib['text']
source.title = outline.attrib['title']
source.feed_type = outline.attrib['type']
source.xml_url = outline.attrib['xmlUrl']
source.html_url = outline.attrib['htmlUrl']
source.save()
user_source = UserSource(user=request.user, source=source)
user_source.save()
return HttpResponseRedirect( reverse('entries') )
else:
form = UploadOpmlFileForm()
return render_to_response('feeds/upload_opml.html', {'form': form}, context_instance=RequestContext(request))
def enterRole(self, ctx):
title = self.__strToken(ctx.QUOTE())
inputstream = ctx.start.getInputStream()
start = ctx.getChild(3).start.start
stop = ctx.getChild(3).stop.stop
text = inputstream.getText(start, stop)
src = Source(title=title, text=text,
owner=self.user.first_name + ' ' + self.user.last_name,
)
src.save()
self.context.append(src)
def enterRole(self, ctx):
title = self.__strToken(ctx.QUOTE())
inputstream = ctx.start.getInputStream()
start = ctx.getChild(3).start.start
stop = ctx.getChild(3).stop.stop
text = inputstream.getText(start, stop)
src = Source(
title=title,
text=text,
owner=self.user.first_name + ' ' + self.user.last_name,
)
src.save()
self.context.append(src)
def source_update(request, pk, template_name='source/source_form.html'):
next_page = request.GET.get('next', None)
source = Source.objects.get(title=pk)
if source == None:
raise Http404("Source does not exist")
if request.method == 'POST':
form = SkipperForm(request.POST)
if form.is_valid():
try:
with transaction.atomic():
# There is no update, sources must be deleted and remade.
# on_delete=CASCADE is emulated, but it works when my objects don't suck.
source.delete()
# Create a new one
source = Source()
source.title = pk
source.text = form.cleaned_data['text']
source.owner = request.user.first_name + ' ' + request.user.last_name
source.save()
# Now build it.
build(user=request.user, sourceobj=source)
except IntegrityError as e:
print "Transaction error:", e
cache.clear()
if form.cleaned_data['next'] != "":
return redirect('jobs', form.cleaned_data['next'])
else:
return redirect('source_list')
else:
return render(request, template_name, {
'title': pk,
'form': form,
'next': next_page
})
else:
form = SkipperForm({'text': source.text, 'title': source.title})
return render(request, template_name, {
'title': pk,
'form': form,
'next': next_page
})
def clone_cohort(request, cohort_id):
if debug: print >> sys.stderr,'Called '+sys._getframe().f_code.co_name
redirect_url = 'cohort_details'
parent_cohort = Cohort.objects.get(id=cohort_id)
new_name = 'Copy of %s' % parent_cohort.name
cohort = Cohort.objects.create(name=new_name)
cohort.save()
# If there are sample ids
samples = Samples.objects.filter(cohort=parent_cohort).values_list('sample_id', 'study_id')
sample_list = []
for sample in samples:
sample_list.append(Samples(cohort=cohort, sample_id=sample[0], study_id=sample[1]))
Samples.objects.bulk_create(sample_list)
# TODO Some cohorts won't have them at the moment. That isn't a big deal in this function
# If there are patient ids
patients = Patients.objects.filter(cohort=parent_cohort).values_list('patient_id', flat=True)
patient_list = []
for patient_code in patients:
patient_list.append(Patients(cohort=cohort, patient_id=patient_code))
Patients.objects.bulk_create(patient_list)
# Clone the filters
filters = Filters.objects.filter(resulting_cohort=parent_cohort).values_list('name', 'value')
# ...but only if there are any (there may not be)
if filters.__len__() > 0:
filters_list = []
for filter_pair in filters:
filters_list.append(Filters(name=filter_pair[0], value=filter_pair[1], resulting_cohort=cohort))
Filters.objects.bulk_create(filters_list)
# Set source
source = Source(parent=parent_cohort, cohort=cohort, type=Source.CLONE)
source.save()
# Set permissions
perm = Cohort_Perms(cohort=cohort, user=request.user, perm=Cohort_Perms.OWNER)
perm.save()
# Store cohort to BigQuery
project_id = settings.BQ_PROJECT_ID
cohort_settings = settings.GET_BQ_COHORT_SETTINGS()
bcs = BigQueryCohortSupport(project_id, cohort_settings.dataset_id, cohort_settings.table_id)
bcs.add_cohort_with_sample_barcodes(cohort.id, samples)
return redirect(reverse(redirect_url,args=[cohort.id]))
def source_update(request, pk, template_name='source/source_form.html'):
next_page = request.GET.get('next', None)
source = Source.objects.get(title=pk)
if source == None :
raise Http404("Source does not exist")
if request.method=='POST':
form = SkipperForm(request.POST)
if form.is_valid():
try:
with transaction.atomic() :
# There is no update, sources must be deleted and remade.
# on_delete=CASCADE is emulated, but it works when my objects don't suck.
source.delete()
# Create a new one
source = Source()
source.title = pk
source.text = form.cleaned_data['text']
source.owner = request.user.first_name + ' ' + request.user.last_name
source.save()
# Now build it.
build(user=request.user, sourceobj=source)
except IntegrityError as e:
print "Transaction error:", e
cache.clear()
if form.cleaned_data['next'] != "" :
return redirect('jobs', form.cleaned_data['next'])
else:
return redirect('source_list')
else:
return render(request, template_name, {'title': pk, 'form':form, 'next': next_page})
else:
form = SkipperForm({'text': source.text, 'title': source.title})
return render(request, template_name, {'title': pk, 'form': form, 'next': next_page})
def save_idea(form):
# process data in form.cleaned_data
title = form.cleaned_data['title']
title_nospaces = str(title.replace(' ', '_').lower())
status = form.cleaned_data['status']
short_desc = form.cleaned_data['short_desc']
long_desc = form.cleaned_data['long_desc']
date_formed = form.cleaned_data['date_formed']
links_strings = form.cleaned_data['links'].split(',')
tags_strings = form.cleaned_data['tags'].split(',')
sources_strings = form.cleaned_data['sources'].split(',')
images_strings = form.cleaned_data['images'].split(',')
# save new idea with cleaned form data
new_idea = Idea(title=title,status=status,short_desc=short_desc,
long_desc=long_desc,date_formed=date_formed)
new_idea.save()
# add links, tags, sources, and images
for link in links_strings:
new_link = Link(url=link)
new_link.save()
new_idea.links.add(new_link)
for tag in tags_strings:
new_tag = Tag(tag=tag)
new_tag.save()
new_idea.tags.add(new_tag)
for source in sources_strings:
new_source = Source(source=source)
new_source.save()
new_idea.sources.add(new_source)
for image in images_strings:
new_image = Image(url=image)
new_image.save()
new_idea.images.add(new_image)
# save after adding data
new_idea.save()
return title
def install():
print("installing templates...")
for template_data in templates:
print("\t{}".format(template_data['name']))
t = Template(template_data)
t.save()
print("installing source texts...")
for source_filename in source_filenames:
source_path = path.join(path.dirname(__file__), 'static/txt', source_filename)
print("\treading {}".format(source_path))
text = open(source_path).read()
s = Source({'name':source_filename,
'text':text,
'uploader': cfg.SYSTEM_USER})
print("\tprocessing {}".format(source_path))
s.process()
print("\tsaving {}".format(source_path))
s.save()
print('adding system user')
u = User({'name':cfg.SYSTEM_USER,
'password': ''})
u.save()
try:
source_method = SourceMethod.objects.get(method_name=s_method)
except SourceMethod.DoesNotExist:
print 'bad method:', s_method
sys.exit(1)
except SourceMethod.DoesNotExist:
print 'bad method id:', s_method
sys.exit(1)
try:
ref = Ref.objects.get(refID=refID)
except Ref.DoesNotExist:
print refID,'does not exist in Ref table!'
sys.exit(1)
print ref.refID, ref.title
try:
source_type = SourceType.objects.get(source_type=ref.ref_type)
except SourceType.DoesNotExist:
print ref.ref_type,'does not exist in SourceType table!'
sys.exit(1)
source = Source(refID=refID, source_type=source_type, authors=ref.authors,
title=ref.title, title_html=ref.title_html, journal=ref.journal,
volume=ref.volume, page_start=ref.page_start,
page_end=ref.page_end, year=ref.year, institution=ref.institution,
note=ref.note, note_html=ref.note_html, doi=ref.doi,
cited_as_html=ref.cited_as_html, url=ref.url,
method=source_method)
source.save()
